mp_decostand-methods: This Function Provideds Several Standardization Methods for...

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

This Function Provideds Several Standardization Methods for Community Data

Description

This Function Provideds Several Standardization Methods for Community Data

Usage

mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

## S4 method for signature 'data.frame'
mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

## S4 method for signature 'MPSE'
mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

## S4 method for signature 'tbl_mpse'
mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

## S4 method for signature 'grouped_df_mpse'
mp_decostand(.data, .abundance = NULL, method = "hellinger", logbase = 2, ...)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the names of otu abundance to be applied standardization.
method	character the name of standardization method, it can one of 'total', 'max', 'frequency', 'normalize', 'range', 'rank', 'rrank', 'standardize' 'pa', 'chi.square', 'hellinger' and 'log', see also decostand
logbase	numeric The logarithm base used in 'method=log', default is 2.
...	additional parameters, see also decostand

Value

update object

Author(s)

Shuangbin Xu

Source

mp_decostand for data.frame object is a wrapper method of vegan::decostand from the vegan package

See Also

[mp_extract_assays()] and [mp_rrarefy()]

decostand

Examples

data(mouse.time.mpse)
mouse.time.mpse %>% 
mp_decostand(.abundance=Abundance, method="hellinger")

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.